This vignette is described as a sample output using hubVis package, one of the applications of Hubverse. By using it the model projections(with quantile data) will be plotted.

For more information about the Hubverse standard format, please refer to the HubDocs website.

2024/02/16 22:31

Plots are generated by applying:

  • “interactive” format: a Plotly output object with interactive legend, hover text, zoom-in and zoom-out options, etc.

Load and Filter Data

The two datasets will be used as an example:

  • example_round1.csv: example of model output for a round associated with the origin date: “2021-03-07” (called “round 1”), target: “incident case”, for the US national level, from the example-complex-scenario-hub. The data set also contains an ensemble calculated by applying the function: hubEnsembles::simple_ensemble(df_round1, agg_fun = "median")

  • rsvnet_hospitalization.csv: example of target data which comes from the rsv-scenario-modeling-ub repo

Load data

Data Preparation

The model output data in the projection_data object follows the structure of the model_out_tbl class. This dataset is converted to a model_out_tbl object after being read-in above. In addition to the standard requirements for this class, the plot_step_ahead_model_output() function in hubVis requires that the dataset have a column whose value corresponds to the variable that should be used for the x-axis of a “step ahead” plot. In general, this should be a date variable that corresponds to the date which is the “target” of a particular prediction. By default it will look for the "target_date" column, although this could be over-ridden by specifying a different column using the x_col_name argument. In our example data, this column does not exist, so we add it below:

Round Results

“Simple” plot

age_groups <- unique(projection_data_all$age_group)
locations <- c("US", "06", "08", "09", "13", "24", "26", "27", "35", "36", "41", "47", "49")

library(htmlwidgets)
library(base64enc)

plot_outputs <- list()
for (age_group in age_groups) {
  for (location in locations) {
        projection_data <- dplyr::filter(projection_data_all,
                                        target == "inc hosp",
                                      age_group == age_group,
                                      location == location)
        truth_data <- dplyr::filter(truth_data_all, 
                                  location == location, 
                                target == "inc hosp", 
                                age_group == age_group, 
                               # time_idx < min(projection_data_ab$target_date),
                                time_idx > "2023-08-01")
        output <- plot_step_ahead_model_output(projection_data, truth_data,
                             show_plot = FALSE,
                             use_median_as_point = TRUE,
                             ens_name = "hub-ensemble", ens_color = "black")
        # 生成したHTMLウィジェットをHTMLファイルに保存します
        temp_file <- tempfile(fileext = ".html")
        # .svg case 
        # temp_file <- tempfile(fileext = ".svg")
        # svg(filename = temp_file)
        saveWidget(output, file = temp_file, selfcontained = FALSE)
        
        # HTMLファイルを読み込み、その内容をBase64エンコードします
        html_data <- readBin(temp_file, "raw", file.info(temp_file)$size)
        encoded_plot <- base64encode(html_data)

        # Base64エンコードされたHTMLをplot_outputsリストに追加します
        plot_outputs[[paste(age_group, location, sep = "_")]] <- encoded_plot
  }
}
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#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> 
#> <div class="dropdown">
#>   <button class="btn btn-default dropdown-toggle" type="button" id="dropdownMenu1" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true">
#>     ドロップダウン
#>     <span class="caret"></span>
#>   </button>
#>   <ul class="dropdown-menu" aria-labelledby="dropdownMenu1">
#>     <li><a href="#">メニュー1</a></li>
#>     <li><a href="#">メニュー2</a></li>
#>     <li><a href="#">メニュー3</a></li>
#>     <li><a href="#">メニュー4</a></li>
#>   </ul>
#> </div>
plot_outputs_json <- jsonlite::toJSON(plot_outputs) #### JavaScriptのコードを作成します js_code <- paste0(”

“)

一時ディレクトリを作成します

temp_dir <- tempfile() dir.create(temp_dir)

htmlDependencyを作成します

html_dependency <- htmltools::htmlDependency( name = “plot_outputs”, version = “1.0”, src=““, script = htmltools::HTML(js_code) #script = sprintf(”var plot_outputs = %s;“, jsonlite::toJSON(plot_outputs)) #src = temp_dir, #script =”plot_outputs.js” ) #### JavaScriptコードを一時ファイルに書き出す #####writeLines(js_code, file.path(html_dependency\(src, html_dependency\)script))

HTML要素を作成します

plot_outputs_div <- htmltools::tags$div(id = “plot_outputs”)

htmlDependencyを追加します

tag_with_dependency <- htmltools::attachDependencies(plot_outputs_div, html_dependency)

htmlDependencyを出力します

htmltools::renderTags(tag_with_dependency)

HTML要素を作成します

dropdowns_div <- htmltools::tags$div(id = “dropdowns”)

htmlDependencyを出力します

htmltools::attachDependencies(dropdowns_div, html_dependency)

By Location

projection_data <- dplyr::filter(projection_data_all, 
                                 age_group ==default_age_group, 
                                 target == default_target,
                                 #model_id == default_model
                                 )
truth_data <- dplyr::filter(truth_data_all,
                            age_group ==default_age_group, 
                            target == default_target,
                              # time_idx < min(projection_data_ab$target_date) ,
                            time_idx > "2023-08-01")
plot_step_ahead_model_output(projection_data, truth_data, 
                             facet = "location_id", 
                             facet_scales = "free_y", 
                             facet_nrow = 7,facet_ncol = 2, 
                             facet_title = "top left", 
                             show_legend = TRUE,
                             ens_name = "hub-ensemble", ens_color = "black")
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken

Layout update

Multiple layout update are possible:

  • Not showing the truth data in the plot:
plot_step_ahead_model_output(projection_data, truth_data_us, 
                             plot_truth = FALSE)
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken

  • Change palette color and behavior:

    • The default palette can be changed. All the available palette names are available here:
    RColorBrewer::display.brewer.all()
plot_step_ahead_model_output(projection_data, truth_data, 
                             pal_color = "Dark2")
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken

It is possible to use only blues for all models, by setting the pal_color parameter to NULL. This might be especially useful when used for many models in conjunction with highlighting the ensemble forecast using the ens_name and ens_color argument.

plot_step_ahead_model_output(projection_data, truth_data, 
                             intervals = 0.8,
                             ens_name = "hub-ensemble", ens_color = "black",
                             pal_color = NULL, use_median_as_point = TRUE)
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken

The default blue color can be changed with the one_color parameter

plot_step_ahead_model_output(projection_data, truth_data, 
                             intervals = 0.8, one_color = "orange",
                             ens_name = "hub-ensemble", ens_color = "black",
                             pal_color = NULL, use_median_as_point = TRUE)
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
plot_step_ahead_model_output(projection_data, truth_data, 
                             interactive = FALSE)
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
  • Column Names:

The input data frames can have different column names for the date information. In this case, the two x_col_name and x_truth_col_name parameters can be used to indicate the variables that should be mapped to the x-axis.

names(truth_data)[names(truth_data) == "time_idx"] <- "time"
names(projection_data)[names(
  projection_data) == "target_date"] <- "date"
plot_step_ahead_model_output(projection_data, truth_data, 
                             x_col_name = "date", x_truth_col_name = "time")
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=min: first taken
#> Warning in reshapeWide(data, idvar = idvar, timevar = timevar, varying =
#> varying, : multiple rows match for output_type_id=max: first taken

Previous Forecasts Archive

Previous weeks’ forecasts are available in the archive and can be accessed in the links below. These forecasts are not updated with updated ground truth data, thus the ground truth data may differ between them as data are back-filled.

Nov 26, 2023 (Epi Week 48)